elements that make up living matter

carbon, oxygen, hydrogen, and nitrogen

phosphorous, sulfur, calcium, potassium

trace elements are required in minute quantities (iron) 

smallest unit of matter that still retains the properties of an element

made up of neutrons, protons, and electrons

neutrons and protons make up the atomic nucleus

protons have a positive charge

electrons have a negative charge 

capacity to cause change

potential energy is the energy an organism has because of its location or structure

electrons have different states of potential energy called energy levels 

attractions that keep atoms together by sharing or transferring valence (outer) electrons

covalent bond is the sharing of a pair of valence electrons  (can be single or double bond)

 nonpolar covalent bond: electrons shared equally

polar covalent bond: electrons shared unequally

ionic bond: formed by attraction of cation (+) and anion (-), forms salts

Hydrogen bond: forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom (for example, the bond between a positive hydrogen in water and a negative nitrogen in ammonia is a hydrogen bond)

Van Der Waals interactions: weak bonds that only occur when atoms and molecules are close together 

H2O is a polar molecule  (oxygen is partially negative, two hydrogens are partially positive)

qualities of water result from hydrogen bonds

cohesion: h-bonds hold water molecules close together (cohesion contributes to the transport of water in plants because an evaporating water molecule will pull another one up along with it and so on throughout the plant)

adhesion: clinging of water to other substances because of h-bonds

(adhesion counters the pull of gravity as wate rmoves up the plant)

surface tension: measure of how difficult it is to stretch or break a liquid, results from collective strength of h-bonds

high specific heat: takes more heat to change its temperature, so water will change temperature less when it absorbs or loses heat (this stabilizes ocean temperatures because water can absorb a huge amount of heat from the sun), it also helps living organisms maintain a stable body temperature than if they were made of a liquid with a lower specific heat

evaporative cooling: water molecules with the most kinetic energy leaves as gas (contributes to stability of temperature in lakes and prevents organisms from overheating)

insulation: water is less dense as a solid (ice) because it expands as it solidifies (h-bonds form crystal lattice) so it can float; it becomes a barrier that protects and insulates the liquid water below to allow life to exist under

 
hydrophilic substances (polar) have an affinity for water

hydrophobic substances (nonpolar) do not have an affinity for water

measure of acidity or basicity of a solution

acid increase hydrogen ion (+) concentration

base decrease hydrogen ion concentration by accepting hydrogen ions or adding hydroxide ions (-) to the solution

7 is a neutral pH

pH less than 7 is acidic

pH greater than 7 is basic 

study of carbon compounds

carbon can form four bonds because for its four valence electrons

hydrocarbons consist of carbon and hydrogen (they are hydrophobic)

isomers are compounds that have the same number of atoms but different structures

structural isomers differ in covalent partners

geometric isomers differ in arrangement around a double bond

enantiomers differ in spatial arrangement 

components involved in chemical reactions 

hydroxyl -OH): alcohols, polar

carbonyl (C=O): ketones (carbonyl group within carbon skeleton), aldehydes (carbonyl group at the end of carbon skeleton), may be structural isomers

carboxyl (COOH): carboxylic acids, acidic properties

amino (NH2): amines, acts as base, picks up protons

sulfhydryl (SH): thiols, 2 SH groups can interact to stabilize protein structure

phosphate (PO4): organic phosphates, makes the molecule of which it is a part an anion, can transfer energy between organic molecules 

carbohydrates, proteins, and nucleic acids are polymers (not fats)

polymers are long molecules consisting of many similar or identical building blocks linked by covalent bonds

 monomers are the building blocks of polymers

condensation (dehydration) reaction results in the synthesis of a polymer by loss of water 

hydrolysis (means to break with water) disassembles polymers into two monomers, a hydrogen from the water attaches to one monomer and a hydroxyl group attaches to the adjacent monomer

monosaccharides (simple sugars), disaccharides (double sugars), polysaccharides (many sugars)

glucose and fructose are monosaccharides (molecular formula is some multible of CH2O)

glycosidic linkage is a covalent bond formed between two monosaccharides by a dehydration reaction (maltose, lactose) 

polysaccharides can serve as storage

starch is the storage form in plants and consists of many glucose polymers

glycogen is the storage form in animals and is kept in the liver and muscle cells, hydrolysis releases glucose

cellulose is a structural polysaccharide that makes up plant cell walls (alpha or beta configuration) 

few animals can digest cellulose (w/o help of bacteria)

although cellulose passes though the digestive tract of humans and is eliminated, it stimulates mucus secretions which aid in smooth passage of food

fat is constructed from glycerol and fatty acids

a fatty acid has a long carbon skeleton with a carboxyl group at one end where the CH chain is attached 

to make a fat, three fatty acid molecules join to glycerol by an ester linkage and the result is a triacylglycerol 

 saturated fats are solid and packed together

unsaturated fats are liquid and packed loosely because of its double bonds

fats function in energy storage as adipose cells

phospholipid has two fatty acids attached to glycerol as the third is joined to a phosphate group; the phosholipid is arranged in a bilayer; it has a hydrophilic phosphate head and 2 hydrophobic tails

steroids are lipids charecterized by a carbon skeleton consisting of four fused rings (cholesterol is a steroid that is a common component of animal cell membranes)

polypeptides are polymers of amino acids

protein consists of one or more polypeptides folded into specific shapes

amino acids have both amino and carboxyl groups

peptide bonds are bonds between amino acids

four levels of protein structure

primary: sequence of amino acids

secondary: alpha helix or beta pleated sheet

tertiary: shape due to interactions b/w side chains (R groups), hydrophobic interactions in the core away from water, van der waals interactions, hydrogen bonds, ionic bonds, and disulfide bridges which rivet parts of protein together

quaternary structure: aggregation of polypeptide subunits, overall structure

chaperonin are protein molecules that assist in proper folding of other proteins by keeping the new polypeptide segregated in a capped cylinder while it folds free from influences in the cytoplasmic environment

denaturation is when a protein unravels and loses its conformation (by heat or chemical agitation), it becomes inactive because the function of a protein depends on its ability to recognize and bind to target molecules 

enzymatic proteins accelerate chemical reactions (digestive enzymes)

structural proteins support the cell (keratin is the protein of hair, feathers, and other skin appendages)

storage proteins store amino acids (casein is the protein of milk and is the source of amino acids for baby mammals)

transport proteins transport substances (hemoglobin transports oxygen)

hormonal proteins coordinate organism's activities (insulin lowers blood sugar level)

receptor proteins respond to chemical stimuli (nerve cell receptors detech signals by other nerve cells)

contractile and motor proteins facilitate movement (actin and myosin responsible for muscle movement)

defensive proteins protect against disease (antibodies attack bacteria and viruses)

DNA  (deoxyribonucleic acid) and RNA (ribonucleic acid)

exists as polymers called polynucleotides, monomer is nucleotide

DNA is the genetic material, unit of inheritence is a gene

Nucleic acids are composed of a sugar-phosphate backbone connected to a nitrogenous base

pyrimidine has a 6-membered ring of carbon and nitrogen (cytosine, thymine, uracil)

purines are larger with 6-membered rings fused to 5-membered rings (adenine and guanine)

pyrimidine binds to purine

DNA forms a double helix, strands run antiparallel (opposite 5'--->3' directions)